three.js/examples/js/loaders/PDBLoader.js

/**
 * @author alteredq / http://alteredqualia.com/
 */

THREE.PDBLoader = function ( manager ) {

	this.manager = ( manager !== undefined ) ? manager : THREE.DefaultLoadingManager;

};

THREE.PDBLoader.prototype = {

	constructor: THREE.PDBLoader,

	load: function ( url, onLoad, onProgress, onError ) {

		var scope = this;

		var loader = new THREE.XHRLoader( scope.manager );
		loader.setCrossOrigin( this.crossOrigin );
		loader.load( url, function ( text ) {

			var json = scope.parsePDB( text );
			scope.createModel( json, onLoad );

		}, onProgress, onError );

	},

	// Based on CanvasMol PDB parser

	parsePDB: function ( text ) {

		function trim( text ) {

			return text.replace(/^\s\s*/, '').replace(/\s\s*$/, '');

		}

		function capitalize( text ) {

			return text.charAt(0).toUpperCase() + text.substr(1).toLowerCase();

		}

		function hash( s, e ) {

			return "s" + Math.min( s, e ) + "e" + Math.max( s, e );

		}

		function parseBond( start, length ) {

			var eatom = parseInt( lines[ i ].substr( start, length ) );

			if ( eatom ) {

				var h = hash( satom, eatom );

				if ( bhash[ h ] == undefined ) {

					bonds.push( [ satom - 1, eatom - 1, 1 ] );
					bhash[ h ] = bonds.length - 1;

				} else {

					// doesn't really work as almost all PDBs
					// have just normal bonds appearing multiple
					// times instead of being double/triple bonds
					// bonds[bhash[h]][2] += 1;

				}

			}

		}

		var CPK = { "h":[ 255,255,255 ],"he":[ 217,255,255 ],"li":[ 204,128,255 ],"be":[ 194,255,0 ],"b":[ 255,181,181 ],"c":[ 144,144,144 ],"n":[ 48,80,248 ],"o":[ 255,13,13 ],"f":[ 144,224,80 ],"ne":[ 179,227,245 ],"na":[ 171,92,242 ],"mg":[ 138,255,0 ],"al":[ 191,166,166 ],"si":[ 240,200,160 ],"p":[ 255,128,0 ],"s":[ 255,255,48 ],"cl":[ 31,240,31 ],"ar":[ 128,209,227 ],"k":[ 143,64,212 ],"ca":[ 61,255,0 ],"sc":[ 230,230,230 ],"ti":[ 191,194,199 ],"v":[ 166,166,171 ],"cr":[ 138,153,199 ],"mn":[ 156,122,199 ],"fe":[ 224,102,51 ],"co":[ 240,144,160 ],"ni":[ 80,208,80 ],"cu":[ 200,128,51 ],"zn":[ 125,128,176 ],"ga":[ 194,143,143 ],"ge":[ 102,143,143 ],"as":[ 189,128,227 ],"se":[ 255,161,0 ],"br":[ 166,41,41 ],"kr":[ 92,184,209 ],"rb":[ 112,46,176 ],"sr":[ 0,255,0 ],"y":[ 148,255,255 ],"zr":[ 148,224,224 ],"nb":[ 115,194,201 ],"mo":[ 84,181,181 ],"tc":[ 59,158,158 ],"ru":[ 36,143,143 ],"rh":[ 10,125,140 ],"pd":[ 0,105,133 ],"ag":[ 192,192,192 ],"cd":[ 255,217,143 ],"in":[ 166,117,115 ],"sn":[ 102,128,128 ],"sb":[ 158,99,181 ],"te":[ 212,122,0 ],"i":[ 148,0,148 ],"xe":[ 66,158,176 ],"cs":[ 87,23,143 ],"ba":[ 0,201,0 ],"la":[ 112,212,255 ],"ce":[ 255,255,199 ],"pr":[ 217,255,199 ],"nd":[ 199,255,199 ],"pm":[ 163,255,199 ],"sm":[ 143,255,199 ],"eu":[ 97,255,199 ],"gd":[ 69,255,199 ],"tb":[ 48,255,199 ],"dy":[ 31,255,199 ],"ho":[ 0,255,156 ],"er":[ 0,230,117 ],"tm":[ 0,212,82 ],"yb":[ 0,191,56 ],"lu":[ 0,171,36 ],"hf":[ 77,194,255 ],"ta":[ 77,166,255 ],"w":[ 33,148,214 ],"re":[ 38,125,171 ],"os":[ 38,102,150 ],"ir":[ 23,84,135 ],"pt":[ 208,208,224 ],"au":[ 255,209,35 ],"hg":[ 184,184,208 ],"tl":[ 166,84,77 ],"pb":[ 87,89,97 ],"bi":[ 158,79,181 ],"po":[ 171,92,0 ],"at":[ 117,79,69 ],"rn":[ 66,130,150 ],"fr":[ 66,0,102 ],"ra":[ 0,125,0 ],"ac":[ 112,171,250 ],"th":[ 0,186,255 ],"pa":[ 0,161,255 ],"u":[ 0,143,255 ],"np":[ 0,128,255 ],"pu":[ 0,107,255 ],"am":[ 84,92,242 ],"cm":[ 120,92,227 ],"bk":[ 138,79,227 ],"cf":[ 161,54,212 ],"es":[ 179,31,212 ],"fm":[ 179,31,186 ],"md":[ 179,13,166 ],"no":[ 189,13,135 ],"lr":[ 199,0,102 ],"rf":[ 204,0,89 ],"db":[ 209,0,79 ],"sg":[ 217,0,69 ],"bh":[ 224,0,56 ],"hs":[ 230,0,46 ],"mt":[ 235,0,38 ],
			   "ds":[ 235,0,38 ],"rg":[ 235,0,38 ],"cn":[ 235,0,38 ],"uut":[ 235,0,38 ],"uuq":[ 235,0,38 ],"uup":[ 235,0,38 ],"uuh":[ 235,0,38 ],"uus":[ 235,0,38 ],"uuo":[ 235,0,38 ] };


		var atoms = [];
		var bonds = [];
		var histogram = {};

		var bhash = {};

		var lines = text.split( "\n" );

		var x, y, z, e;

		for ( var i = 0, il = lines.length; i < il; ++ i ) {

			if ( lines[i].substr(0, 4) == "ATOM" || lines[i].substr(0, 6) == "HETATM" ) {

				x = parseFloat( lines[i].substr(30, 7) );
				y = parseFloat( lines[i].substr(38, 7) );
				z = parseFloat( lines[i].substr(46, 7) );

				e = trim( lines[i].substr(76, 2) ).toLowerCase();

				if ( e == "" ) e = trim(lines[i].substr(12, 2)).toLowerCase();
				atoms.push( [ x,y,z, CPK[e], capitalize(e) ] );

				if (histogram[e] == undefined) histogram[e] = 1;
				else histogram[e] += 1;

			} else if (lines[i].substr(0, 6) == "CONECT") {

				var satom = parseInt( lines[i].substr(6, 5) );

				parseBond(11, 5);
				parseBond(16, 5);
				parseBond(21, 5);
				parseBond(26, 5);

			}

		}

		return { "ok": true, "atoms": atoms, "bonds": bonds, "histogram": histogram };

	},

	createModel: function ( json, callback ) {

		var scope = this,
		geometryAtoms = new THREE.Geometry(),
		geometryBonds = new THREE.Geometry();

		geometryAtoms.elements = [];

		var atoms = json.atoms;
		var bonds = json.bonds;

		for ( var i = 0; i < atoms.length; i ++ ) {

			var atom = atoms[ i ];

			var x = atom[ 0 ];
			var y = atom[ 1 ];
			var z = atom[ 2 ];

			var position = new THREE.Vector3( x, y, z );
			geometryAtoms.vertices.push( position );

			var r = atom[ 3 ][ 0 ] / 255;
			var g = atom[ 3 ][ 1 ] / 255;
			var b = atom[ 3 ][ 2 ] / 255;

			var color = new THREE.Color();
			color.setRGB( r, g, b );

			geometryAtoms.colors.push( color );

			geometryAtoms.elements.push( atom[ 4 ] );

		}

		for ( var i = 0; i < bonds.length; i ++ ) {

			var bond = bonds[ i ];

			var start = bond[ 0 ];
			var end = bond[ 1 ];

			var vertex1 = geometryAtoms.vertices[ start ];
			var vertex2 = geometryAtoms.vertices[ end ];

			geometryBonds.vertices.push( vertex1.clone() );
			geometryBonds.vertices.push( vertex2.clone() );

		}

		callback( geometryAtoms, geometryBonds, json );

	}

};